Chemotaxis of Bdellovibrio bacteriovorus toward pure compounds

Bacterial amino acid chemotaxis: a widespread strategy with multiple physiological and ecological roles

Chemotaxis is the directed, flagellum-based movement of bacteria in chemoeffector gradients. Bacteria respond chemotactically to a wide range of chemoeffectors, including amino, organic, and fatty acids, sugars, polyamines, quaternary amines, purines, pyrimidines, aromatic hydrocarbons, oxygen, inorganic ions, or polysaccharides. Most frequent are chemotactic responses to amino acids (AAs), which were observed in numerous bacteria regardless of their phylogeny and lifestyle. Mostly chemoattraction responses are observed, although a number of bacteria are repelled from certain AAs. Chemoattraction is associated with the important metabolic value of AAs as growth substrates or building blocks of proteins. However, additional studies revealed that AAs are also sensed as environmental cues. Many chemoreceptors are specific for AAs, and signaling is typically initiated by direct ligand binding to their four-helix bundle or dCache ligand-binding domains. Frequently, bacteria possess multiple AA-responsive chemoreceptors that at times possess complementary AA ligand spectra. The identification of sequence motifs in the binding sites at dCache_1 domains has permitted to define an AA-specific family of dCache_1AA chemoreceptors. In addition, AAs are among the ligands recognized by broad ligand range chemoreceptors, and evidence was obtained for chemoreceptor activation by the binding of AA-loaded solute-binding proteins. The biological significance of AA chemotaxis is very ample including in biofilm formation, root and seed colonization by beneficial bacteria, plant entry of phytopathogens, colonization of the intestine, or different virulence-related features in human/animal pathogens. This review provides insights that may be helpful for the study of AA chemotaxis in other uncharacterized bacteria.

Distinct dynamics and proximity networks of hub proteins at the prey-invading cell pole in a predatory bacterium

In bacteria, cell poles function as subcellular compartments where proteins localize during specific lifecycle stages, orchestrated by polar "hub" proteins. Whereas most described bacteria inherit an "old" pole from the mother cell and a "new" pole from cell division, generating cell asymmetry at birth, non-binary division poses challenges for establishing cell polarity, particularly for daughter cells inheriting only new poles. We investigated polarity dynamics in the obligate predatory bacterium Bdellovibrio bacteriovorus, proliferating through filamentous growth followed by non-binary division within prey bacteria. Monitoring the subcellular localization of two proteins known as polar hubs in other species, RomR and DivIVA, revealed RomR as an early polarity marker in B. bacteriovorus. RomR already marks the future anterior poles of the progeny during the predator's growth phase, during a precise period closely following the onset of divisome assembly and the end of chromosome segregation. In contrast to RomR's stable unipolar localization in the progeny, DivIVA exhibits a dynamic pole-to-pole localization. This behavior changes shortly before the division of the elongated predator cell, where DivIVA accumulates at all septa and both poles. In vivo protein interaction networks for DivIVA and RomR, mapped through endogenous miniTurbo-based proximity labeling, further underscore their distinct roles in cell polarization and reinforce the importance of the anterior "invasive" cell pole in prey-predator interactions. Our work also emphasizes the precise spatiotemporal order of cellular processes underlying B. bacteriovorus proliferation, offering insights into the subcellular organization of bacteria with filamentous growth and non-binary division.IMPORTANCEIn bacteria, cell poles are crucial areas where "hub" proteins orchestrate lifecycle events through interactions with multiple partners at specific times. While most bacteria exhibit one "old" and one "new" pole, inherited from the previous division event, setting polar identity poses challenges in bacteria with non-binary division. This study explores polar proteins in the predatory bacterium Bdellovibrio bacteriovorus, which undergoes filamentous growth followed by non-binary division inside another bacterium. Our research reveals distinct localization dynamics of the polar proteins RomR and DivIVA, highlighting RomR as an early "hub" marking polar identity in the filamentous mother cell. Using miniTurbo-based proximity labeling, we uncovered their unique protein networks. Overall, our work provides new insights into the cell polarity in non-binary dividing bacteria.

Advances in cellular and molecular predatory biology of Bdellovibrio bacteriovorus six decades after discovery

Since its discovery six decades ago, the predatory bacterium Bdellovibrio bacteriovorus has sparked recent interest as a potential remedy to the antibiotic resistance crisis. Here we give a comprehensive historical overview from discovery to progressive developments in microscopy and molecular mechanisms. Research on B. bacteriovorus has moved from curiosity to a new model organism, revealing over time more details on its physiology and fascinating predatory life cycle with the help of a variety of methods. Based on recent findings in cryo-electron tomography, we recapitulate on the intricate molecular details known in the predatory life cycle including how this predator searches for its prey bacterium, to how it attaches, grows, and divides all from within the prey cell. Finally, the newly developed B. bacteriovorus progeny leave the prey cell remnants in the exit phase. While we end with some unanswered questions remaining in the field, new imaging technologies and quantitative, systematic advances will likely help to unravel them in the next decades.

The role of mathematical modelling in understanding prokaryotic predation

With increasing levels of antimicrobial resistance impacting both human and animal health, novel means of treating resistant infections are urgently needed. Bacteriophages and predatory bacteria such as Bdellovibrio bacteriovorus have been proposed as suitable candidates for this role. Microbes also play a key environmental role as producers or recyclers of nutrients such as carbon and nitrogen, and predators have the capacity to be keystone species within microbial communities. To date, many studies have looked at the mechanisms of action of prokaryotic predators, their safety in in vivo models and their role and effectiveness under specific conditions. Mathematical models however allow researchers to investigate a wider range of scenarios, including aspects of predation that would be difficult, expensive, or time-consuming to investigate experimentally. We review here a history of modelling in prokaryote predation, from simple Lotka-Volterra models, through increasing levels of complexity, including multiple prey and predator species, and environmental and spatial factors. We consider how models have helped address questions around the mechanisms of action of predators and have allowed researchers to make predictions of the dynamics of predator-prey systems. We examine what models can tell us about qualitative and quantitative commonalities or differences between bacterial predators and bacteriophage or protists. We also highlight how models can address real-world situations such as the likely effectiveness of predators in removing prey species and their potential effects in shaping ecosystems. Finally, we look at research questions that are still to be addressed where models could be of benefit.

Bacterial Predation on Cyanobacteria

Predatory bacteria gained interest in the last 20 years. Nevertheless, only a few species are well characterized. The endobiotic predator Bdellovibrio bacteriovorus invades its prey to consume it from the inside, whereas Myxococcus xanthus hunts as a whole group to overcome its prey. Both species were described to prey on cyanobacteria as well. This minireview summarizes the findings of the last 20 years of predatory bacteria of cyanobacteria and is supplemented by new findings from a screening experiment for bacterial predators of the model organism Anabaena variabilis PCC 7937. Known predatory bacteria of cyanobacteria belong to the phyla Proteobacteria, Bacteroidetes, and Firmicutes and follow different hunting strategies. The underlying mechanisms are in most cases not known in much detail. Isolates from the screening experiment were clustered after predation behaviour and analyzed with respect to their size. The effect of predation in high nitrate levels and the occurrence of nitrogen-fixing cells, called heterocysts, are addressed.

Effects of the prey landscape on the fitness of the bacterial predators Bdellovibrio and like organisms

Bdellovibrio and like organisms (BALOs) are obligate predatory bacteria commonly encountered in the environment. In dual predator-prey cultures, prey accessibility ensures optimal feeding and replication and rapid BALO population growth. However, the environmental prey landscape is complex, as it also incorporates non-prey cells and other particles. These may act as decoys, generating unproductive encounters which in turn may affect both predator and prey population dynamics. In this study, we hypothesized that increasing decoy:prey ratios would bring about increasing costs on the predator's reproductive fitness. We also tested the hypothesis that different BALOs and decoys would have different effects. To this end, we constructed prey landscapes including periplasmic or epibiotic predators including two types of decoy under a large range of initial decoy:prey ratio, and mixed cultures containing multiple predators and prey. We show that as decoy:prey ratios increase, the maximal predator population sizes is reduced and the time to reach it significantly increases. We found that BALOs spent less time handling non-prey (including superinfection-immune invaded prey) than prey cells, and did not differentiate between efficient and less efficient prey. This may explain why in multiple predator and prey cultures, less preferred prey appear to act as decoy.

Phylogenomic Insights into Distribution and Adaptation of Bdellovibrionota in Marine Waters

Bdellovibrionota is composed of obligate predators that can consume some Gram-negative bacteria inhabiting various environments. However, whether genomic traits influence their distribution and marine adaptation remains to be answered. In this study, we performed phylogenomics and comparative genomics studies using 132 Bdellovibrionota genomes along with five metagenome-assembled genomes (MAGs) from deep sea zones. Four phylogenetic groups, Oligoflexia, Bdello-group1, Bdello-group2 and Bacteriovoracia, were revealed by constructing a phylogenetic tree, of which 53.84% of Bdello-group2 and 48.94% of Bacteriovoracia were derived from the ocean. Bacteriovoracia was more prevalent in deep sea zones, whereas Bdello-group2 was largely distributed in the epipelagic zone. Metabolic reconstruction indicated that genes involved in chemotaxis, flagellar (mobility), type II secretion system, ATP-binding cassette (ABC) transporters and penicillin-binding protein were necessary for the predatory lifestyle of Bdellovibrionota. Genes involved in glycerol metabolism, hydrogen peroxide (H2O2) degradation, cell wall recycling and peptide utilization were ubiquitously present in Bdellovibrionota genomes. Comparative genomics between marine and non-marine Bdellovibrionota demonstrated that betaine as an osmoprotectant is probably widely used by marine Bdellovibrionota, and all the marine genomes have a number of genes for adaptation to marine environments. The genes encoding chitinase and chitin-binding protein were identified for the first time in Oligoflexia, which implied that Oligoflexia may prey on a wider spectrum of microbes. This study expands our knowledge on adaption strategies of Bdellovibrionota inhabiting deep seas and the potential usage of Oligoflexia for biological control.

Statistical signatures of a targeted search by bacteria

Chemoattractant gradients are rarely well-controlled in nature and recent attention has turned to bacterial chemotaxis toward typical bacterial food sources such as food patches or even bacterial prey. In environments with localized food sources reminiscent of a bacterium's natural habitat, striking phenomena-such as the volcano effect or banding-have been predicted or expected to emerge from chemotactic models. However, in practice, from limited bacterial trajectory data it is difficult to distinguish targeted searches from an untargeted search strategy for food sources. Here we use a theoretical model to identify statistical signatures of a targeted search toward point food sources, such as prey. Our model is constructed on the basis that bacteria use temporal comparisons to bias their random walk, exhibit finite memory and are subject to random (Brownian) motion as well as signaling noise. The advantage with using a stochastic model-based approach is that a stochastic model may be parametrized from individual stochastic bacterial trajectories but may then be used to generate a very large number of simulated trajectories to explore average behaviors obtained from stochastic search strategies. For example, our model predicts that a bacterium's diffusion coefficient increases as it approaches the point source and that, in the presence of multiple sources, bacteria may take substantially longer to locate their first source giving the impression of an untargeted search strategy.

Catch me if you can: dispersal and foraging of Bdellovibrio bacteriovorus 109J along mycelia

To cope with heterogeneous environments and resource distributions, filamentous fungi have evolved a spatially extensive growth enabling their hyphae to penetrate air-water interfaces and pass through air-filled pores. Such mycelia are also known to act as dispersal networks for the mobilisation of bacteria ('fungal highways') and connection of microbial microhabitats. Hitherto, however, nothing is known about the effect of mycelia-based dispersal on interactions between bacterial predators and their prey and concomitant effects on biomass formation. We here hypothesise that mycelia enable the contact between predators and their prey and shape a prey's population. We investigated the impact of predation by Bdellovibrio bacteriovorus 109J on the growth of its potential prey Pseudomonas fluorescens LP6a in the presence of mycelia. Our data give evidence that hyphae increase the accessibility of the prey to B. bacteriovorus 109J and, hence, allow for efficient foraging and shaping of prey populations not seen in the absence of mycelia. To test our hypothesis tailored microbial landscapes were used for better reduction of emerging properties in complex systems. Our data suggest that mycelia have substantial influence on prey-predator relationship and hereby may promote the structure of prey and predator populations and, hence, may be a determinant for biomass formation in heterogeneous environments.

Isolation and classification of Bdellovibrio and like organisms

Bdellovibrio and like organisms (BALOs) are obligate predators of Gram-negative bacteria. BALOs are isolated as plaques growing at the expense of their prey and are cultivated as two-member cultures. The growth cycle is composed of an extracellular attack phase and an intraperiplasmic elongation and replication phase. However, there are methods for obtaining host-independent (HI) mutants that grow without prey on rich media. BALOs are commonly found in the environment but generally constitute small populations; therefore, their isolation may require enrichment steps. Contamination by other bacteria during isolation necessitates efficient separation between the smaller BALO cells from the majority of larger bacteria. BALOs can also be directly detected and quantified in environmental samples using specific PCR. Synchronous cultures of both wild-type and HI derivatives can be obtained to study the different growth phases. These can be further separated by centrifugation. Classification is based on 16S rDNA analysis. Protocols relevant to these aspects of BALO detection, isolation, growth, classification, and quantitation are presented in this unit.

The chemical-in-plug bacterial chemotaxis assay is prone to false positive responses

Background

Chemical-in-plug assays are commonly used to study bacterial chemotaxis, sometimes in the absence of stringent controls.

Results

We report that non-chemotactic and non-motile mutants in two distinct bacterial species (Shewanella oneidensis and Helicobacter pylori) show apparent zones of accumulation or clearing around test plugs containing potential attractants or repellents, respectively.

Conclusions

Our results suggest that the chemical-in-plug assay should be used with caution, that non-motile or non-chemotactic mutants should be employed as controls, and that results should be confirmed with other types of assays.

Characterization of type IV pili in the life cycle of the predator bacterium Bdellovibrio

Bdellovibrio and like organisms (BALOs) are obligate prokaryotic predators of other Gram-negative bacteria. Bdellovibrio bacteriovorus is the most studied organism among BALOs. It has a periplasmic life cycle with two major stages: a motile, non-replicative stage spent searching for prey (the attack phase) and a stage spent inside the periplasm of the Gram-negative prey cell (the growth phase) after forming an osmotically stable body termed the bdelloplast. Within Bdellovibrio, there are also strains exhibiting an epibiotic life cycle. The genome sequence of the type strain B. bacteriovorus HD100(T) revealed the presence of multiple dispersed pil genes encoding type IV pili. Type IV pili in other bacteria are involved in adherence to and invasion of host cells and therefore can be considered to play a role in invasion of prey cells by Bdellovibrio. In this study, genes involved in producing type IV pili were identified in the periplasmic strain B. bacteriovorus 109J and an epibiotic Bdellovibrio sp. strain JSS. The presence of fibres on attack-phase cells was confirmed by examining negative stains of cells fixed with 10% buffered formalin. Fibres were at the non-flagellated pole on approximately 25% of attack-phase cells. To confirm that these fibres were type IV pili, a truncated form of PilA lacking the first 35 amino acids was designed to facilitate purification of the protein. The truncated PilA fused to a His-tag was overexpressed in Escherichia coli BL21(DE3) plysS. The fusion protein, accumulated in the insoluble fraction, was purified under denaturing conditions and used to produce polyclonal antisera. Immunoelectron microscopy showed that polar fibres present on the cell surface of the predator were composed of PilA, the major subunit of type IV pili. Immunofluorescence microscopy showed the presence of pilin on attack-phase cells of B. bacteriovorus 109J during attachment to prey cells and just after penetration, inside the bdelloplast. Antibodies against PilA delayed and inhibited predation in co-cultures of Bdellovibrio. This study confirms that type IV pili play a role in invasion of prey cells by Bdellovibrio.

Development of a novel system for isolating genes involved in predator-prey interactions using host independent derivatives of Bdellovibrio bacteriovorus 109J

BACKGROUND

Bdellovibrio bacteriovorus is a gram-negative bacterium that preys upon other gram-negative bacteria. Although the life cycle of Bdellovibrio has been extensively investigated, very little is known about the mechanisms involved in predation.

RESULTS

Host-Independent (HI) mutants of B. bacteriovorus were isolated from wild-type strain 109J. Predation assays confirmed that the selected HI mutants retained their ability to prey on host cells grown planktonically and in a biofilm. A mariner transposon library of B. bacteriovorus HI was constructed and HI mutants that were impaired in their ability to attack biofilms were isolated. Transposon insertion sites were determined using arbitrary polymerase chain reaction. Ten HI transposon mutants mapped to genes predicted to be involved in mechanisms previously implicated in predation (flagella, pili and chemotaxis) were further examined for their ability to reduce biofilms.

CONCLUSION

In this study we describe a new method for isolating genes that are required for Bdellovibrio biofilm predation. Focusing on mechanisms that were previously attributed to be involved in predation, we demonstrate that motility systems are required for predation of bacterial biofilms. Furthermore, genes identified in this study suggest that surface gliding motility may also play a role in predation of biofilms consistent with Bdellovibrios occupying a biofilm niche. We believe that the methodology presented here will open the way for future studies on the mechanisms involved in Bdellovibrio host-prey interaction and a greater insight of the biology of this unique organism.

Predatory mechanisms of Bdellovibrio and like organisms

Bdellovibrio and like organisms (BALOs) are predatory, Gram-negative delta-proteobacteria with a complex developmental lifecycle. In the free-living attack phase they are highly motile and seek out prey bacteria that they invade. The ensuing intracellular growth and replication is characterized by the development of a long filament that septates into individual cells that differentiate further into the flagellated attack-phase bacterium. The prey bacterium is lysed and motile predators are released. BALOs have recently been considered to have potential as living antibiotics. The idea of using predatory bacteria as therapeutic agents to combat pathogenic Gram-negative bacteria is intriguing, as they can prey upon human pathogenic bacteria including Salmonella, Pseudomonas and Escherichia coli. However, our current knowledge of the amazing biology of these prokaryotes that cause the systematic destruction of Gram-negative bacteria is still rather limited. More has to be learned about their predatory lifestyle before their application as therapeutic agents will become feasible.

Response of Bdellovibrio and Like Organisms (BALOs) to the Migration of Naturally Occurring Bacteria to Chemoattractants

A dual culture-based and non-culture-based approach was applied to characterize predator bacterial groups in surface water samples collected from Apalachicola Bay, Florida. Chemotaxis drop assays were performed on concentrated samples in an effort to isolate predator bacteria by their chemotactic ability. Yeast extract (YE) and casamino acids (CA) proved to be strong chemoattractants and resulted in three visibly distinct bands; however, dextrose, succinate, pyruvate, and concentrated cells of Vibrio parahaemolyticus P5 as prey did not elicit any response. The three distinct bands from YE and CA were separately collected to identify the chemotactic microbial assemblages. Plaque-forming unit assays from different chemotaxis bands with P5 as prey indicated 5- (CA) to 10-fold (YE) higher numbers of predator bacteria in the outermost chemotactic bands. Polymerase chain reaction-restriction fragment length polymorphism and 16S rDNA sequencing of clones from different chemotaxis bands resulted in identification of Pseudoalteromonas spp., Marinomonas spp., and Vibrio spp., with their numbers inversely proportional to the numbers of predators-i.e., Bdellovibrio spp. and Bacteriovorax spp-in the chemotaxis bands. This study indicates that predatorial bacteria potentially respond to high densities of microbial biomass in aquatic ecosystems and that chemotaxis drop assay may be an alternate culture-independent method to characterize predatorial bacterial guilds from the environment.

Bdellovibrio: growth and development during the predatory cycle

Predatory Bdellovibrio enter the periplasm of other Gram-negative bacteria, growing within and consuming them. Unravelling molecular details of this intimate association between bacterial predator and prey is challenging yet fascinating, and might lead to novel antibacterials in the future. Pioneering physiological and biochemical studies described the predatory life of Bdellovibrio in the 1960s and 1970s, later followed by recombinant DNA work in the 1990s, which led to a revival in Bdellovibrio molecular research. This revival continues in the 21st century with the advent of a genome sequence. Now worldwide research is underway on the comparative genomics and transcriptomics of predatory bacteria, and will illuminate the evolutionary adaptations to become predatory, and will hopefully ultimately illuminate how the predatory processes of Bdellovibrio can be employed against pathogenic bacteria and for humankind.

Chemotactic responses to metals and anaerobic electron acceptors in Shewanella oneidensis MR-1

Although a previous study indicated that the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 lacks chemotactic responses to metals that can be used as anaerobic electron acceptors, new results show that this bacterium responds to both Mn(III) and Fe(III). Cells were also shown to respond to another unusual electron acceptor, the humic acid analog anthraquinone-2,6-disulfonate. These results indicate that S. oneidensis is capable of moving towards a number of unusual anaerobic electron acceptors, including some that would normally be insoluble in the environment. Additionally, S. oneidensis was shown to migrate in gradients of several divalent cations under anaerobic conditions. Although responses to the reduced forms of redox-active metals, such as Mn(II) and Fe(II), might indicate that S. oneidensis uses gradients of these metals to locate the insoluble electron acceptors Mn(III/IV) and Fe(III) for dissimilatory purposes, responses to non-redox-active metals, such as Zn(II), suggest that movement towards divalent cations might serve other, potentially assimilatory, purposes.

Predation, death, and survival in a biofilm: Bdellovibrio investigated by atomic force microscopy

Biofilms are complex microbial communities that are resistant to attack by bacteriophages and to removal by drugs and chemicals. Here we use atomic force microscopy (AFM) to image the attack on Escherichia coli biofilms by Bdellovibrio bacteriovorus 109J. Bdellovibrio is a small, predatory bacterium that invades and devours other Gram-negative bacteria. We demonstrate that under dilute nutrient conditions, bdellovibrios can prevent the formation of simple bacterial biofilms and destroy established biofilms; under richer conditions the prey bacteria persist and are not eradicated, but may be shifted toward solution populations. Using AFM we explore these bacterial interactions with more detail and accuracy than available by more traditional staining assays or optical microscopy. AFM also allows us to investigate the nanoscale morphological changes of the predator, especially those related to motility. This demonstration of Bdellovibrio's successful predation in a biofilm inspires us to consider ways that it might be used productively for industrial, medical, agricultural, and biodefensive purposes.

Downregulation of the motA gene delays the escape of the obligate predator Bdellovibrio bacteriovorus 109J from bdelloplasts of bacterial prey cells

Bdellovibrio bacteriovorus is a Gram-negative bacterium that preys on other Gram-negative bacteria. The lifecycle of B. bacteriovorus alternates between an extracellular flagellated and highly motile non-replicative attack-phase cell and a periplasmic non-flagellated growth-phase cell. The prey bacterium containing periplasmic bdellovibrios becomes spherical but osmotically stable, forming a structure known as the bdelloplast. After completing the growth phase, newly formed bdellovibrios regain their flagellum and escape the bdelloplast into the environment, where they encounter more prey bacteria. The obligate predatory nature of B. bacteriovorus imposes a major difficulty to introducing mutations in genes directly involved in predation, since these mutants could be non-viable. This work reports the cloning of the B. bacteriovorus 109J motAB operon, encoding proteins from the flagellar motor complex, and a genetic approach based on the expression of a motA antisense RNA fragment to downregulate motility. Periplasmic bdellovibrios carrying the plasmid expressing antisense RNA displayed a marked delay in escaping from bdelloplasts, while the released attack-phase cells showed altered motility. These observations suggest that a functionally intact flagellar motor is required for the predatory lifecycle of B. bacteriovorus. Also, the use of antisense RNA expression may be a useful genetic tool to study the Bdellovibrio developmental cycle.

The incidence of Bdellovibrio spp. in man-made water systems: coexistence with legionellas

Bdellovibrios have been isolated from surface waters but there are no reports of its occurrence in mains water supplies. One hundred and thirty five water samples from 81 sources were examined for the presence of Bdellovibrio bacteriovorus and Legionella spp. Bdellovibrios were isolated by a double-layer agar technique with two strains of Legionella pneumophila serogroup 1 as the host organisms. Bdellovibrio spp. were isolated from 57.8% and Legionella spp. from 9.5% of the samples. The two species occurred together in 4.4% of samples. The incidence of Bdellovibrio spp. and its occurrence with legionellas in man-made water systems is discussed.